A day in the life of a PhD student. Chapter 5.

As a PhD student, I often get asked the question ‘So what do you do?’

A simple enough question. A simple enough answer of ‘I research embryonic stem cells and how they use oxygen concentration and glycolysis, a type of metabolism, to stay as stem cells’.

But sometimes I then get asked ‘No! I mean what do you do in a typical day?’

Again, a simple enough question. But probably a little more complicated to answer. There is not typical day as a PhD student working in the lab – you just do whatever experiments need doing – or perhaps whatever experiments your cells allow you to do! Because of this variety coupled with my want to be able to explain a usual day for me, it resulted in this ‘A day in the life of a PhD student’ feature. A snippet into my days in the lab to show how varied by work is.

So I thought it was time to show another day – especially now I am starting to do some new experiments that I can introduce to you. So – welcome to Chapter 5 of ‘A Day in the Life of a PhD student’.

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8:03am – The worst time of day – the alarm call! But now that the clocks have gone back, it is making getting up in the mornings that little bit easier as it is brighter outside! But it’s only making it a little bit easier!

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9:27am – So I have been in work a good 20 minutes already and Windows is STILL configuring updates! With lab meeting starting in 3 minutes time, I gave up my quest to check emails this morning and just headed into the lab and started some experiments that could be running whilst I’m in meetings this morning.

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9:31am – So my new experiments are looking at the DNA of my embryonic stem cells. We want to find out if a certain protein is switching on the expression of my gene of interest in my stem cells and I am doing this using ChIP. Now I’m not eating crisps or fries depending on where you are in the world, but instead ChIP stands for chromatin immunoprecipitation assay. Basically what this experiment does is extract all the DNA from my cells in the form of chromatin – which is DNA with all of its associated proteins still attached. Feel free to ask me some more questions about chromatin but for this post we will leave it at that and delve into it deeper in another blog post at a later date. Anyway, once the chromatin is free from the cell we chop it up into smaller fragments and then add an antibody that will bind to our certain protein. We then move onto the precipitation step. We use magnetic beads that will bind to the antibody and bring with it anything that the antibody has bound to – so hopefully the protein and some DNA. After a few more steps, we want to see if our certain protein is bound to a specific DNA sequence which it would have pulled out of the solution with it when we added the magnetic beads.

This procedure though needs several days work just to get one result and today is the second day so probably won’t make much sense, But what I am starting this morning is the steps to check if my chromatin has been chopped up enough – which we will see later.

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11:27am – On to the second meeting of the morning. The first one was the whole lab meeting. We have these usually once a week just so we can all catch up on what everyone is doing, see if anyone needs any help with any issues they may be having and discussing any problems or things that need to be dealt with.

For my second meeting of the morning, I had booked in my supervisor to discuss more specifically what I have been up to in the lab and what other experiments needed to be done. The result was that I need one more result before I can submit a manuscript for my first paper which hopefully can be submitted by the end of the summer. Fingers crossed all goes well. So apart from discussing what experiments I need to do ASAP, we also divulged into what I would be starting after that to hopefully get paper number 2 (and number 3 hopefully!) before I graduate with my PhD. As I have never published in a journal before, discussions lead on to where I even begin to look for where to submit to and all this complicated business so if anyone has any advice it would be greatly appreciated!

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1:14pm – In the window I had between meetings, I started the steps to develop my Western blot which I have discussed in more detail in Chapter 4 of this feature. So now it was time to add my developer fluid and run over to my second home – the dark room – to see if my western blot had worked or not.

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2:40pm – So, this morning I started preparing my ChIP samples to analyse whether I had chopped up my chromatin enough. And we analyse this by running the samples on a gel! Now – if you have read my other blogs in this feature, this might seem a little familiar to you! Back in Chapter 1 I showed you how I start a Western blot and run a gel to separate proteins. Well, this is what I am doing here but with a different type of gel. Proteins are much, much bigger in size compared to DNA so this gel is thicker and has smaller ‘holes’ so even something as small as DNA can be separated by how long it is. But much like the gels I use for Western blotting, I still have to make the gels which is what I am doing here.

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2:42pm – This particular gel is made by adding some powder called agarose to a buffer and then heating it in a microwave to help the powder to dissolve.

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2:46pm – Once the agarose was dissolved and the solution had been cooled slightly, the liquid was poured into the mould, a comb added so there was spaces to add my samples later on and it was allowed to set.

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2:53pm – While I am waiting for my gel to set, my Western blot had worked so it was time to probe it for beta actin expression. This protein’s expression stays the same no matter what conditions you inflict on your cells because it makes up part of your cell’s skeleton – called the cytoskeleton – and it helps to stop your cell caving it on itself. So it’s expression never changes because your cell always needs the same amount of actin. But we probe for it’s expression in a Western blot as it is our housekeeping gene. It checks that we have loaded the same amount of protein per sample and so any changes we see in the expression of our protein of interest is sue to some biological reason and not just because I accidentally loaded more protein into one well compared to another.

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3:07pm – Gel is all set. Samples were loaded in the well left by removing the comb which you can see with the green rectangles in the gel. And we are ready to click GO and let the DNA separate by size just like the proteins do in a Western blot.
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3:16pm – While that is running it is time to grab a (very) late lunch! Didn’t bring any lunch with me from home so popped across to the shop! Followed by the obligatory daily Facebook browse whilst munching away at my desk and stopping my stomach from rumbling anymore!

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4:15pm – Gel has finished running so now it is time to image my gel and see whether my DNA has been chopped up enough. So when I was making the gel I added in a dye that binds to DNA and then glows under UV light to reveal where my DNA is in the gel. Here, I’ve put my gel on a UV light box which will show me those all important results.

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4:18pm – One good result and one bad result! So the two columns on the left hand side are my size markers. So I need to run these alongside my samples to know what size the DNA is otherwise it would have been pointless running my gel. The two columns on the right are my samples. They both have basically appeared as smears because when I chop up my DNA for the ChIP assay it is totally random so in theory there is all different sizes of all different sequences shown here. But you can see the right hand sample shows a bigger smear which goes higher up the gel. The higher up the gel, the bigger the pieces of DNA. So unfortunately this sample has not chopped up my DNA into small enough pieces compared to the sample on the left.

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4:27pm – So although one of my samples hasn’t been chopped up enough, I thought it was probably best to measure the DNA concentration in both samples in case I can use it, or I can chop up the DNA some more. So we do this using a spectrophotometer called the Nanodrop. This tells you how much DNA is in the sample by measuring how much UV light is absorbed at certain wavelengths.

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5:06pm – So today I am running very behind schedule due to both meetings over running this morning – but I’ll soldier on as science never stops! Spending a few minutes writing up my lab book, catching up on emails, ordering reagents and labelling my Western blots ready for analysis.

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5:21pm – It’s that time of day again – feeding time! For any newbies to my blog I work on embryonic stem cells and they are proper divas of the cell world! We try and keep them happy by feeding them every single day so they don’t differentiate! I have written a post before about feeding my cells so check that out here if you want to know some more about that!

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5:43pm – All lab work is done for the day! But now for the paperwork! I’ve got to write up everything in my lab book and also put any new data into my data file so I can make graphs and test for significance! But I am also quite a visual learner so after all the discussion I had with my supervisor in our meeting this morning, I wanted to put that into more of a diagram for both the cell types I am working on to compare similarities and differences. I also wanted to map out the gaps I have and think about the experiments I need to finish that or at least start finding out what is going on in these pesky cells!

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5:50pm – Home time! Very glad for my 30 second walk home right now! Really tired today!

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6:46pm – So after a bit of a binge watching crap on TV, dinner is prepped and in the oven so I thought I would try and be a little productive this evening. I’m going on holiday next week 🙂 so thought it was about time to check out what clothes I had, and more importantly which of those fit me, and started to make piles of shoes, toiletries and other things I might need to bring. I finished with starting to prepare my hand luggage pile which is going to go in my this new backpack I bought and am actually in love with!

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8:22pm – Dinner eaten! Putting off doing the washing up by watching the Masters! Chilling for the rest of the evening before heading back into the lab tomorrow 🙂

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What is a typical day like for you and your science research?Please share your stories so anyone who reads this blog can see how varied a scientist’s day can be! It is not lab 9am-5pm Monday to Friday.

I hope you enjoyed another insight into my life as a PhD student. Please feel free to ask my any questions you might have about what I’ve written about today or my work in general if you like.

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Please don’t forget to keep up to date on all my new blog posts, all the latest news and more! Find me and Soph talks Science on Facebook, Twitter and Instagram.

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